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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ), 'gf_id' => 'HOM05D001483', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001483' ), 'data_identifier' => 'HOM05D001483', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001483', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '428', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p14190' => 'bna', 'A05p00180' => 'bna', 'A07p32580' => 'bna', 'Aa31LG1G29120' => 'aar', 'Aa31LG5G15900' => 'aar', 'Aa31LG7G9830' => 'aar', 'Aa31sc377G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4791' => 'aag', 'Actinidia09652' => 'ach', 'Actinidia16811' => 'ach', 'Actinidia20709' => 'ach', 'Actinidia24337' => 'ach', 'Actinidia32230' => 'ach', 'Actinidia35562' => 'ach', 'Ah.03g136160' => 'amhyb', 'Ah.04g161140' => 'amhyb', 'AL2G25910' => 'aly', 'AL3G16100' => 'aly', 'AL4G47360' => 'aly', 'Aqoxy5G00725' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12N6X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6TI0EB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZTS91' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SXJ33X' => 'arhy', 'AT1G67360' => 'ath', 'AT2G47780' => 'ath', 'AT3G05500' => 'ath', 'ATR0561G268' => 'atr', 'ATR0796G074' => 'atr', 'Atru.chr11.2322' => 'acertr', 'Atru.chr5.1177' => 'acertr', 'AUR62000766' => 'cqu', 'AUR62005203' => 'cqu', 'AUR62005619' => 'cqu', 'AUR62008664' => 'cqu', 'AUR62024111' => 'cqu', 'AUR62033105' => 'cqu', 'BcaB02g08746' => 'bca', 'BcaB03g15350' => 'bca', 'BcaB04g21447' => 'bca', 'BcaB05g24272' => 'bca', 'BcaB05g24273' => 'bca', 'BcaB05g24278' => 'bca', 'BcaC02g12542' => 'bca', 'BcaC03g14838' => 'bca', 'BcaC05g30116' => 'bca', 'BcaC05g30162' => 'bca', 'BcaC09g47829' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00030' => 'bna', 'BolC1t05692H' => 'bol', 'BolC2t08443H' => 'bol', 'BolC4t21657H' => 'bol', 'BolC5t34831H' => 'bol', 'BolC6t38962H' => 'bol', 'BraA05t19014Z' => 'bra', 'BraA05t19072Z' => 'bra', 'BraA07t30882Z' => 'bra', 'BraSC132t45501Z' => 'bra', 'C02p22990' => 'bna', 'C04p00100' => 'bna', 'C05p61720' => 'bna', 'C05p61730' => 'bna', 'C06p38730' => 'bna', 'CAN.G1459.8' => 'can', 'CAN.G339.29' => 'can', 'CAN.G43.15' => 'can', 'CAN.G875.8' => 'can', 'CANSAT01G2055' => 'cansat', 'CANSAT54G0666' => 'cansat', 'CARHR059900' => 'chi', 'CARHR079890' => 'chi', 'CARHR143150' => 'chi', 'CARHR143170' => 'chi', 'Carub.0002s1365' => 'cru', 'Carub.0003s0479' => 'cru', 'Carub.0004s3049' => 'cru', 'Ca_00327_v3' => 'car', 'Ca_16460_v3' => 'car', 'Ca_18035_v3' => 'car', 'Ca_18538_v3' => 'car', 'CBR_g18704' => 'cbr', 'CBR_g36719' => 'cbr', 'Cc01_g20690' => 'ccan', 'Cc02_g34030' => 'ccan', 'Cc03_g10150' => 'ccan', 'Cc11_g16880' => 'ccan', 'CDE02G2679' => 'cde', 'CDE05G1419' => 'cde', 'CDE11G1119' => 'cde', 'Cfa005942' => 'cfa', 'Cfa006626' => 'cfa', 'Cfa009368' => 'cfa', 'Cfa013419' => 'cfa', 'Ciclev10003627m.g' => 'ccl', 'Ciclev10003772m.g' => 'ccl', 'Ciclev10022084m.g' => 'ccl', 'Ciclev10032648m.g' => 'ccl', 'CiPaw.05G110000' => 'cil', 'CiPaw.06G102500' => 'cil', 'CiPaw.07G021300' => 'cil', 'CiPaw.08G162100' => 'cil', 'ClCG03G017110' => 'cla', 'ClCG11G013690' => 'cla', 'COL.COLO4_10516' => 'col', 'COL.COLO4_14032' => 'col', 'COL.COLO4_20399' => 'col', 'COL.COLO4_23370' => 'col', 'COL.COLO4_29005' => 'col', 'Cpa.g.sc43.55' => 'cpa', 'Cpa.g.sc48.93' => 'cpa', 'Cpa.g.sc9.214' => 'cpa', 'CsaV3_1G038850' => 'csa', 'CsaV3_5G030300' => 'csa', 'CSS0003911' => 'camsi', 'CSS0011748' => 'camsi', 'CSS0019490' => 'camsi', 'CSS0021527' => 'camsi', 'CSS0025133' => 'camsi', 'CSS0037379' => 'camsi', 'CSS0048035' => 'camsi', 'DCAR_002819' => 'dca', 'DCAR_003355' => 'dca', 'DCAR_005804' => 'dca', 'DCAR_005805' => 'dca', 'DCAR_018333' => 'dca', 'DCAR_022147' => 'dca', 'Dinv10958' => 'din', 'Dinv17561' => 'din', 'Dinv19712' => 'din', 'Dinv30806' => 'din', 'Dinv40340' => 'din', 'Duzib106G1142' => 'dzi', 'Duzib106G1680' => 'dzi', 'Duzib128G1195' => 'dzi', 'Duzib133G1257' => 'dzi', 'Duzib177G1003' => 'dzi', 'Duzib268G0839' => 'dzi', 'ECA233G2699' => 'eca', 'ECA233G4747' => 'eca', 'ECA247G2851' => 'eca', 'EL10Ac3g07222' => 'bvu', 'EL10Ac4g09918' => 'bvu', 'EL10Ac5g11773' => 'bvu', 'EL10Ac6g13501' => 'bvu', 'Eucgr.B01915' => 'egr', 'Eucgr.H04640' => 'egr', 'Eucgr.K03465' => 'egr', 'FAN02G1573' => 'fan', 'FAN05G4514' => 'fan', 'FAN07G0712' => 'fan', 'FAN07G2420' => 'fan', 'FAN12G1210' => 'fan', 'FAN14G4146' => 'fan', 'FAN15G2501' => 'fan', 'FAN15G3652' => 'fan', 'FAN17G1457' => 'fan', 'FAN17G2562' => 'fan', 'FAN19G2805' => 'fan', 'FAN20G0333' => 'fan', 'FAN22G1802' => 'fan', 'FAN23G0358' => 'fan', 'FAN23G0527' => 'fan', 'FAN24G2312' => 'fan', 'FAN26G2621' => 'fan', 'FAN27G2431' => 'fan', 'FAN28G0012' => 'fan', 'FvH4_1g23500' => 'fve', 'FvH4_2g25450' => 'fve', 'FvH4_4g23780' => 'fve', 'FvH4_4g23790' => 'fve', 'FvH4_6g06530' => 'fve', 'Glyma.05G147200' => 'gma', 'Glyma.07G195800' => 'gma', 'Glyma.08G104200' => 'gma', 'Glyma.11G250500' => 'gma', 'Glyma.13G180500' => 'gma', 'Glyma.13G240100' => 'gma', 'Glyma.15G073200' => 'gma', 'Glyma.18G006700' => 'gma', 'Gohir.A01G158200' => 'ghi', 'Gohir.A03G126300' => 'ghi', 'Gohir.A04G139500' => 'ghi', 'Gohir.A11G267900' => 'ghi', 'Gohir.A11G294800' => 'ghi', 'Gohir.A12G131800' => 'ghi', 'Gohir.D01G147700' => 'ghi', 'Gohir.D02G149300' => 'ghi', 'Gohir.D04G182700' => 'ghi', 'Gohir.D11G131950' => 'ghi', 'Gohir.D11G277800' => 'ghi', 'Gohir.D11G309500' => 'ghi', 'Gohir.D12G135466' => 'ghi', 'Gohir.D12G135500' => 'ghi', 'Gorai.002G183700' => 'gra', 'Gorai.005G167200' => 'gra', 'Gorai.007G141100' => 'gra', 'Gorai.007G300000' => 'gra', 'Gorai.007G341500' => 'gra', 'Gorai.008G146600' => 'gra', 'Gorai.008G146700' => 'gra', 'Gorai.012G175700' => 'gra', 'GSVIVG01010480001' => 'vvi', 'GSVIVG01027980001' => 'vvi', 'GSVIVG01031148001' => 'vvi', 'HanXRQChr04g0117011' => 'han', 'HanXRQChr08g0207791' => 'han', 'HanXRQChr10g0284611' => 'han', 'HanXRQChr11g0339251' => 'han', 'HanXRQChr11g0339301' => 'han', 'HanXRQChr11g0339731' => 'han', 'HanXRQChr11g0339741' => 'han', 'HanXRQChr13g0394341' => 'han', 'HanXRQChr15g0465721' => 'han', 'Haze_04142' => 'cav', 'Haze_04904' => 'cav', 'Haze_12417' => 'cav', 'Hma1.2p1_0142F.1_g064320' => 'hma', 'Hma1.2p1_0209F.1_g088550' => 'hma', 'Hma1.2p1_0391F.1_g142850' => 'hma', 'Hma1.2p1_1212F.1_g267280' => 'hma', 'HPP92_006924' => 'vpl', 'HPP92_010674' => 'vpl', 'HPP92_010697' => 'vpl', 'Hund07095' => 'sun', 'Hund21709' => 'sun', 'Hund25464' => 'sun', 'Lalb_Chr08g0230631' => 'lal', 'Lalb_Chr13g0294311' => 'lal', 'Lalb_Chr15g0089851' => 'lal', 'Lalb_Chr16g0383711' => 'lal', 'Lalb_Chr18g0059681' => 'lal', 'Lalb_Chr23g0278021' => 'lal', 'Lj1A28T43' => 'lonja', 'Lj3C1068T4' => 'lonja', 'Lj4g0013589' => 'lja', 'Lj5A421T58' => 'lonja', 'Lj6A826T52' => 'lonja', 'Lj6A826T53' => 'lonja', 'Lj6C826T5' => 'lonja', 'Lj6g0001795' => 'lja', 'Lj6g0011839' => 'lja', 'Lju2527A1T29' => 'lonja', 'Lsat_1_v5_gn_0_32660' => 'lsa', 'Lsat_1_v5_gn_8_147461' => 'lsa', 'Lsat_1_v5_gn_8_147700' => 'lsa', 'Lsat_1_v5_gn_9_1021' => 'lsa', 'Lsat_1_v5_gn_9_87781' => 'lsa', 'Lsat_1_v5_gn_9_87820' => 'lsa', 'Lsat_1_v5_gn_9_87841' => 'lsa', 'Lsat_1_v5_gn_9_87901' => 'lsa', 'Lsat_1_v5_gn_9_88040' => 'lsa', 'Lsat_1_v5_gn_9_88221' => 'lsa', 'Lsat_1_v5_gn_9_88241' => 'lsa', 'Lsat_1_v5_gn_9_88301' => 'lsa', 'Manes.05G063700' => 'mes', 'Manes.08G117800' => 'mes', 'Manes.09G170000' => 'mes', 'Manes.12G011500' => 'mes', 'Manes.13G012400' => 'mes', 'Mapoly0008s0002' => 'mpo', 'Mapoly0054s0059' => 'mpo', 'MBI18_g21821_MAGBIO' => 'mbi', 'MBI19_g12137_MAGBIO' => 'mbi', 'MD01G1161800' => 'mdo', 'MD03G1285600' => 'mdo', 'MD04G1201000' => 'mdo', 'MD08G1165600' => 'mdo', 'MD11G1305000' => 'mdo', 'MD12G1213500' => 'mdo', 'MD13G1118800' => 'mdo', 'MD16G1119000' => 'mdo', 'Medtr1g055235' => 'mtr', 'Medtr2g013440' => 'mtr', 'Medtr3g085370' => 'mtr', 'Medtr4g088915' => 'mtr', 'Medtr8g080570' => 'mtr', 'MELO3C011868.2' => 'cme', 'MELO3C015310.2' => 'cme', 'Migut.E00019' => 'egut', 'Migut.N01499' => 'egut', 'Migut.N02080' => 'egut', 'MSTRG.12603' => 'ama', 'MSTRG.17413' => 'ama', 'MSTRG.2459' => 'ama', 'MSTRG.27982' => 'ama', 'MSTRG.506' => 'ama', 'MSTRG.8002' => 'ama', 'Nitab4.5_0000060g0050' => 'nta', 'Nitab4.5_0000619g0100' => 'nta', 'Nitab4.5_0001404g0050' => 'nta', 'Nitab4.5_0003658g0030' => 'nta', 'Nitab4.5_0003901g0030' => 'nta', 'Nitab4.5_0004891g0020' => 'nta', 'Nn3g21444' => 'nnu', 'Oeu010917.1' => 'oeu', 'Oeu012117.1' => 'oeu', 'Oeu012119.1' => 'oeu', 'Oeu036872.1' => 'oeu', 'Oeu047449.1' => 'oeu', 'Oeu058922.1' => 'oeu', 'Os05g0151300' => 'osa', 'Os07g0671800' => 'osa', 'Peaxi162Scf00037g01117' => 'pax', 'Peaxi162Scf00067g02520' => 'pax', 'Peaxi162Scf00128g01227' => 'pax', 'Peaxi162Scf00518g00425' => 'pax', 'PGR044G2695' => 'pgr', 'PGR083G1598' => 'pgr', 'PGSC0003DMG400011370' => 'stu', 'PGSC0003DMG400024708' => 'stu', 'PGSC0003DMG400029107' => 'stu', 'Phvul.001G261800' => 'pvu', 'Phvul.002G228100' => 'pvu', 'Phvul.006G186300' => 'pvu', 'Phvul.L001946' => 'pvu', 'Potri.001G055300' => 'ptr', 'Potri.002G206000' => 'ptr', 'Potri.003G173100' => 'ptr', 'Potri.005G025700' => 'ptr', 'Potri.013G017300' => 'ptr', 'Pp3c19_21240' => 'ppa', 'Prupe.1G226000' => 'ppe', 'Prupe.6G321100' => 'ppe', 'Prupe.8G258700' => 'ppe', 'Psat0s2314g0080' => 'psa', 'Psat1g205480' => 'psa', 'Psat5g096240' => 'psa', 'Psat7g112520' => 'psa', 'PSO017G1179' => 'pso', 'PSO017G1353' => 'pso', 'PSO017G5042' => 'pso', 'PSO170G2785' => 'pso', 'PSO210G0621' => 'pso', 'PSO302G0291' => 'pso', 'PSO478G0003' => 'pso', 'PSO478G2951' => 'pso', 'PSO478G3993' => 'pso', 'PSO675G6283' => 'pso', 'PSO832G1773' => 'pso', 'QL03p021016' => 'qlo', 'QL03p021851' => 'qlo', 'QL03p052770' => 'qlo', 'QL12p027182' => 'qlo', 'QL12p029239' => 'qlo', 'RcHm_v2.0_Chr2g0118901' => 'rch', 'RcHm_v2.0_Chr2g0144991' => 'rch', 'RcHm_v2.0_Chr3g0455691' => 'rch', 'RcHm_v2.0_Chr4g0430271' => 'rch', 'RcHm_v2.0_Chr4g0430281' => 'rch', 'RcHm_v2.0_Chr6g0293681' => 'rch', 'Rhsim07G0187800' => 'rsi', 'Rhsim12G0025900' => 'rsi', 'Rhsim12G0099400' => 'rsi', 'Rhsim13G0012200' => 'rsi', 'Sabra01G0039900' => 'sbr', 'Sabra02G0153400' => 'sbr', 'Sabra03G0126600' => 'sbr', 'Sabra13G0016300' => 'sbr', 'Sabra13G0020300' => 'sbr', 'SalBow2G0646' => 'sbo', 'SalBow2G3366' => 'sbo', 'SalBow8G2469' => 'sbo', 'Sc04g0010120' => 'sci', 'Sc05g0004180' => 'sci', 'Sc16g0008650' => 'sci', 'Sed0008682' => 'sed', 'Sed0021381' => 'sed', 'Sed0023952' => 'sed', 'SEGI_26185' => 'sgi', 'SGA_v2.0_scaffold1G00393' => 'sas', 'SGA_v2.0_scaffold2G01417' => 'sas', 'SGA_v2.0_scaffold36G14353' => 'sas', 'SGA_v2.0_scaffold391G50635' => 'sas', 'SGA_v2.0_scaffold5095G54592' => 'sas', 'SGA_v2.0_scaffold65G22171' => 'sas', 'SGA_v2.0_scaffold87G27155' => 'sas', 'SHI18106' => 'shi', 'SMO116G0274' => 'smo', 'SMO356G0415' => 'smo', 'Solyc01g099680.3' => 'sly', 'Solyc05g015390.3' => 'sly', 'Solyc09g074930.3' => 'sly', 'Sopen01g043190' => 'spe', 'Sopen03g014600' => 'spe', 'Sopen05g010680' => 'spe', 'Sopen09g029750' => 'spe', 'Sp3g04330' => 'spa', 'Sp4g29710' => 'spa', 'Sp5g22310' => 'spa', 'TAR622G0546' => 'tar', 'TAR633G0028' => 'tar', 'TAR633G2427' => 'tar', 'TAR636G1635' => 'tar', 'THA.LOC104802166' => 'tha', 'THA.LOC104807878' => 'tha', 'THA.LOC104817620' => 'tha', 'THA.LOC104825508' => 'tha', 'Thecc.01G297600' => 'tca', 'Thecc.02G209100' => 'tca', 'Thecc.05G312700' => 'tca', 'Thhalv10001614m.g' => 'esa', 'Thhalv10019076m.g' => 'esa', 'Thhalv10021402m.g' => 'esa', 'TPR.G17067' => 'tpr', 'TPR.G29047' => 'tpr', 'TPR.G33049' => 'tpr', 'TPR.G7715' => 'tpr', 'TWI12G0384' => 'twi', 'TWI12G1324' => 'twi', 'TWI14G0138' => 'twi', 'TWI36G0031' => 'twi', 'TWI36G0558' => 'twi', 'TWI56G0117' => 'twi', 'TWI59G0901' => 'twi', 'TWI75G1387' => 'twi', 'TWI75G1813' => 'twi', 'unitig_21.g20040' => 'ugi', 'unitig_26.g10396' => 'ugi', 'unitig_26.g9484' => 'ugi', 'unitig_8.g3137' => 'ugi', 'vmacro01332' => 'vma', 'vmacro02465' => 'vma', 'vmacro16107' => 'vma', 'VMungo0251G1711' => 'vmu', 'VMungo0251G2771' => 'vmu', 'VMungo0540G2228' => 'vmu', 'Zm00001eb111200' => 'zma', 'Zm00001eb354140' => 'zma' ) $gf_id = 'HOM05D001483' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001483' ) $data_identifier = 'HOM05D001483' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 1, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 2, 'cqu' => (int) 6, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 2, 'camsi' => (int) 7, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 19, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 7, 'lja' => (int) 3, 'lsa' => (int) 12, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 1, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 11, 'qlo' => (int) 5, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 9, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354140' $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